Algorithmic Specified Complexity in the Game of Life, revisited

In 2015, Winston Ewert, William Dembski and Robert Marks published a paper entitled Algorithmic Specified Complexity in the Game of Life.

The paper was a wreck. We examined it here at TSZ and found well over 20 substantive errors in it.

ID supporter Eric Holloway describes it as a “neat paper”. I describe it as an “abysmal mess”.

Eric has been touting the virtues of ASC here at TSZ, so now is a good time to reopen the discussion of this paper.

No cloning theorem: the double edge sword

Essentially, there are 2 types of cloning…

Biological cloning leading to clones such as identical twins who share exactly the same DNA.

Or artificial, genetically engineered cloning leading to such clones as plants whose DNA is also identical.

But there exists a more precise kind of cloning in physics that reaches all the way to the subatomic level of particles. Everything in the universe is made up of elementary quantum particles and the forces by which they interact, including DNA and us. This kind of cloning is more detailed because it involves the superposition of subatomic particles; their relative positions (particles can be in more than 1 position or state at the time), momenta and energy levels of every particle and all of their bonds and interactions are exactly the same in the copy (clone) as the original.

This kind of perfect cloning is impossible. It has been proven mathematically and formulated into the no cloning theorem, which states:

“In physics, the no-cloning theorem states that it is impossible to create an identical copy of an arbitrary unknown quantum state.”

How those two types of cloning apply to life systems, such as us, our DNA and so forth?

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A list of things for which CSI has been determined

Intelligent Design advocates are still talking about CSI and determining the value of it.

CSI measures whether an event X is best explained by a chance hypothesis C, or some specification S.

So I’d like this thread to be a list of biological entities and the value of CSI that has been determined for each.

If no entries are made then I believe that would demonstrate that CSI might measure X Y or Z but it never actually has done so.

Out of interest, what is the CSI of a bacterial flagellum?

Examples of “Pathological Idiocy” in Universities, Especially in Social Sciences and Related Disciplines

It is an embarrassment to be associated with the academy when pathological idiocy of this sort is published and cited in the same manner as genuine intellectual/scientific endeavor… What the hell is wrong with us? — Jordan Peterson, Tweet with link to paper

One can follow the hyperlink to see what Peterson was specifically talking about (I didn’t quote from the paper Peterson was criticizing since it was too vulgar). But more generally, in a recording (which might already be deleted from the net), Peterson praised the RealPeerReview twitter website that highlighted some of the publications of the academics which Peterson was likely also referring to when he used the phrase “pathological idiocy.”

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Genetic code is a programming language

Specifically, it looks like the genetic code is a LISP dialect.

Operon structure of genetic code:
https://s3-us-west-2.amazonaws.com/courses-images/wp-content/uploads/sites/1094/2016/11/03164740/OSC_Microbio_11_07_Operon.jpg

LISP function structure:
http://support.ircam.fr/docs/om/om6-manual/res/listprefix.png

Nested genes:
https://player.slideplayer.com/31/9782148/data/images/img11.jpg

Nested LISP cons cells:
https://www.tutorialspoint.com/lisp/images/treestructure.jpg

Science Uprising: Who wins the battle over mind?

The scientific evidence for immaterial mind defeats materialism – claims Dr. Egnor, a neurosurgeon affiliated with the Discovery Institute… Not so quickly – says Dr. Faizal Ali, a psychiatrist affiliated with CAMH and University of Toronto, who describes himself as an anti-creationist and a militant atheist. He believes that neural networks can be responsible for the emergence of the human mind, naturally…

Let’s look at their evidence…

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Echo Chambers & Epistemic Bubbles

This article might help some people make better sense of what goes on around here. https://aeon.co/essays/why-its-as-hard-to-escape-an-echo-chamber-as-it-is-to-flee-a-cult

Unarguably, young earth creationism (YECism) was & still is an echo chamber. It’s a shock to YECists when then get out of their common circles to hear statistically higher educated Christians than they are speaking about how compatible accepting limited biological evolutionary theories with their religious faith actually is. So when they get out of their echo chamber and realize that learning and research hasn’t stopped but rather continues, even among their fellow religious, that they didn’t know existed, it can have a chilling or liberating effect.

The Intelligent Design movement with its Intelligent Design theory/ideology (IDism) was & still is an echo chamber, based, governed & funded in Seattle, USA. I’d welcome an open conversation with Stephen C. Meyer & John G. West about this. Indoctrination going one way is all they’ve focused on, while indoctrination going the other way is an elephant in the room that IDists will eventually need to come around to address.

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Origins Debates

Given the ideological opposition by the site’s founder to having ‘debates’ as a way of making progress or solving disagreements over at Peaceful Science (https://discourse.peacefulscience.org/, “In my view, science is not up for public debate.”) on topics related to human and life origins, I wonder what the attitudes of people towards ‘origins debates’ are here at TSZ. Do you call it ‘the Creation Wars’ as S. Joshua Swamidass does?

Below are a few questions for those who do not wish to play by Swamidass’ rules and who indeed, don’t mind putting their ideas, knowledge and ability to answer challenges to their theories, dogmas and biases, to the test in debate. It’s not like Joshua can actually defend ‘methodological naturalism’ other than with multiple falsehoods and having to sell his ‘Me-Scientist’ piety badge at a discount. So, let us imagine a hypothetical and suppose a ‘friendly debate’ were possible to construct and see if anyone here can play along. These are survey questions about a ‘debate’ that many people seem willing to admit they are themselves already engaged in here and elsewhere.

Questions:

1. When considered as not only a discussion, but rather as a ‘debate,’ what is/are the key debate topic(s) over human & life origins really about?

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Discrete versus Gradualism

  1. Gradualism is the cornerstone of Darwin’s Theory of Evolution because without it, he could not justify the idea that one organism changes into another. ‘Gradualism’ equals ‘Continuity’ but also presupposes a significant change, not just variations around a static mean (regression to the mean).
  2. In math, a function is gradual if continuous. A continuous function has a Grade’ (Slope) at every point. If a function is not gradual (continuous), then it is Discrete and has no ‘Grade’ (Slope). A Discontinuous function is a special case of ‘Continuous over limited ranges’. Some argue that large collections of discrete points appear continuous, thus justifying gradualism. This view were acceptable if and only if the contribution of the discrete points were strictly cumulative (such as when many water molecules form water waves). 
  3. Is Nature Gradual? No, Nature is Discrete from the most elementary particles, to molecules, cells, and organisms. New organisms are created by discrete processes and result in newborns that are measurably different from each parent while all DNA mutations are discrete events. Gregor Mendel observed the discrete nature of biology as early as 1865 in the inheritance of dominant and recessive alleles. Darwin might have learned that from Mendel’s papers sent to him, had he read and correctly interpreted the results. To be fair, Darwin’s gradualism was in line with the incorrect view of his times that considered matter a continuum. Only in the late 1800s the true discrete nature of matter started to become common knowledge. However, today everyone knows, yet the gradualism hypothesis remains central to evolution despite lacking any basis.
  4. The list of discrete elements in biology includes but is not limited to: atoms, molecules, biochemical reactions, DNA, RNA, proteins, enzymes, genes, chromosomes, organelles, cell types (pro/eukaryote), cell division (mitosis/meiosis), sex type (male/female), body organs, organ systems, and organism classification. Changes at the discrete micro level including mutations and exposure to free radicals, radiation, and misfolded proteins are not cumulative and can potentially impact the entire organism. Continuous measure such as temperature, volume and weight are not true biologic properties as these change over the life of organisms and are primarily statistical measures at population level in particular populations, environments and time.    
  5. We classify organisms into distinct groups with little if any overlap and with significant homogeneity within the group. If Gradualism were the norm, all living animals would fill a continuous spectrum which would make their classification in various taxa completely arbitrary. Were gradualism true in time – call this vertical gradualism, then gradualism over the current living – horizontal gradualism – should also be the norm. Instead, we observe that even unicellular organisms with huge populations and short-lived generations do not occupy a biological continuum. Plant diversity over the altitude & latitude continuum is a good example of Discontinuity in Nature: as conditions change, we see a changing mix of distinct species, rather than hybrid species as would be expected if Gradualism were true. Animal territoriality is also an example of discrete successful designs dominating certain ranges and mixing with each other at range boundaries without significantly changing their characteristics. 
  6. What about Speciation and Hybridization? And what about the Fossil Record?  A certain flexibility appears built into each biological design – more in some than in others. What we call Speciation and Hybridization may in fact be no more than adaptations within these flexibility ranges. Without confirming experiments on living organisms, it is impossible to determine whether the Fossil Record shows Gradualism or instead predisposition to Gradualism prompts an incorrect interpretation of the Fossil Record.
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Evolutionary textbooks need rewriting again. Why not scrap them to save trees?

Each time I stumble upon a provocative article like this it makes me wonder what makes one so certain that for one evolutionary failure another evolutionary bluff is going to be the answer… Is it the blind and absolute commitment to materialism?

How multi-celled animals developed. Evolutionary discovery to rewrite text books

“New findings challenge the long-standing idea that multi-celled animals evolved from a single-celled ancestor resembling a modern sponge cell known as a choanocyte.”

Biologists for decades believed the existing theory was a no-brainer, as sponge choanocytes look so much like single-celled choanoflagellates — the organism considered to be the closest living relatives of the animals,” she said.

“But their transcriptome signatures simply don’t match, meaning that these aren’t the core building blocks of animal life that we originally thought they were.

This technology has been used only for the last few years, but it’s helped us finally address an age-old question, discovering something completely contrary to what anyone had ever proposed.”

“We’re taking a core theory of evolutionary biology and turning it on its head,” she said.

“Now we have an opportunity to re-imagine the steps that gave rise to the first animals, the underlying rules that turned single cells into multicellular animal life.”

Now, the Darwinian Police and the damage control and propaganda machine are going to get busy… The strategy never changes though:

“To us it looks like it could have evolved, so it must have evolved.” The “HOW” it evolved issue is never addressed and the testing of the hypothesis always remains in the realm of speculative, evolutionary science…

On how convergence of form , where one form’s origin is proven, makes any other option for the origin of other forms, very low on a probability curve.

In geomorphology/geology, and in biology I discovered that forms of something are cl;aimed to have had different origins. In geomorphology, just three examples, are how great canyons were agreed to have been caused by a megaflood in one day, like the mIssoula flood and others, that completely mimic what other canyons look like but are said to have been created over great timelines even millions of years. Another case is how salt stagimites(sp) , created instantly in a day or so, look exactly like other stagimites , made of other elements, that are claimed to have taken large timelines, thousands of years, in caves to grow. then in meteorites they have found tiny tiny diamonds(I think in meteorites) that they conclude were created instantly, a moment, from great heat/pressure WHILE still saying regular bigger diamonds were created from long timelines, millions of years.In biology there is the famous convergent cases of marsupials looking spot on like non marsupials in forms like dogs, cats, mice.

I say that in all these cases its not just that having proven a origin for one form that allows us to say its the origin for any like form BUT that on a probability curve its very unlikely that the origin hypothesis for the forms, not proven/witnessed , are right. not just unneeded but very prompting they were wrong. they were speculations about long timelines that were used until modern investigation proved, for like firms ,were rapidly created.That in these cases real time math/probability really can correct errors that are in opposition to creationism.

Teleology in mindless BIBO stable cybernetic machines, compartmentalizing ID/Creation arguments

One definition I found for teleology:

the explanation of phenomena in terms of the purpose they serve rather than of the cause by which they arise.

An example of a mindless machine that can be described in terms of teleology is an autopilot or missile guidance system. “The purpose of an autopilot or guidance system is to drive the vehicle to its destination.” One does not immediately have to invoke non-material minds for this proximal description of the system. In fact, no one would say there is a non-material spirit inside a missile guidance system. For that reason, any system exhibiting purposeful behavior (or dare we say moral-like behavior) cannot by default be assumed to have non-material soul.

Conflating core ID and Creation Science with issues of materialism just adds confusion factors. IDists and Creationists can talk about notions of a non-material soul, even some quantum physicists have hinted at it, but such discussions should be compartmentalized outside of core ID and creation science arguments that are built on analysis of probability. Perhaps questions of soul should be compartmentalized to the realm of unprovable faith statements.

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Christian List on free will

For many people, the idea of free will is bound up with the notion of “could have done otherwise”. By their lights, if only one future is possible for a person — that is, if the person cannot do otherwise — then free will is an illusion.

Philosopher Christian List — author of the recent book Why Free Will is Real — proposes an interesting species of free will based on the claim that while physics may be deterministic, behaviors at the agent level are not. Agents can do otherwise, according to List, and this is enough to ground free will even if physics is deterministic.

I think List is mistaken, but I’ll save my criticisms for the comment thread.

Readers can find List’s argument in this paper:

Free Will, Determinism, and the Possibility of Doing Otherwise

See you in the comment thread.

Moral luck

It’s Saturday night and you’re at a party.  You drink too much and foolishly decide to drive home.  On the way, you lose control of your car.  Then one of two things happens:

Scenario A

There is no traffic around.  Your out-of-control car careens across the left lane and into a ditch.  It hits a fence post.  The car is damaged, but you are unhurt.  The police come  and arrest you for driving under the influence.

Scenario B

A car is approaching.  Your out-of-control car careens across the left lane and clips the oncoming car, which crashes into a tree.  The driver and her two young children are killed.  The police come and arrest you.  You are charged with manslaughter.

The crucial difference between the two scenarios is sheer luck.  In scenario A, you were simply lucky that no traffic was around.  In scenario B, your luck wasn’t as good, and three people ended up dead.

You made the same irresponsible decision — to drink and drive — in both scenarios.  Is your moral culpability greater in scenario B than in scenario A?  If so, why?

Evolution affirms the Consequent

  1. Affirming the Consequent is a logical fallacy that takes a known true statement [if P then Q] and invalidly concludes its converse [if Q then P]:
    1. If Bill Gates owns Fort Knox, then Bill Gates is rich. Bill Gates is rich. Therefore, Bill Gates owns Fort Knox. False!
    2. If an animal is a dog, then it has four legs. My cat has four legs. Therefore, my cat is a dog. False!
    3. If it’s raining, then the streets are wet. The streets are wet. Therefore it’s raining. False! It could be raining or it could be something else. The “therefore” claim is false.
  2. How does ‘Affirming the consequent’ apply to evolution? We have not observed “evolution”. No one has, and no one will, despite the effort (see LTEE). What was observed is Resemblance, the Birth Mechanism, Variability and Adaptability. Neither of these (even combined) can logically be extrapolated to “evolution”, namely the hypothesized transmutation of one type of organism into another. Proofs of “evolution” always take the form: If “evolution” is true, then XYZ is true. XYZ is true. Therefore “evolution” is true. This is a classical Affirming the Consequent logical fallacy.
  3. Let’s see some concrete examples of “proof of evolution” fallacies:
    • If “evolution” is true, some fossils are ancestors of and therefore resemble existing organisms. Fossils resemble one another and existing organisms. Therefore “evolution” is true. This argument fails because there will always be some resemblance between two or more entities (even chairs and cats have four legs in general). Also, a fossil can always be from an unrelated branch of the “tree of life” which circularly presupposes “evolution” anyway.
    • If “evolution” is true, organisms are genetically similar. Organisms are genetically similar. Therefore “evolution” is true. This argument is false because other hypotheses such as common design account for genetic similarities just as well.
    • If “evolution” is true, one might expect common embryology. Similar organisms have similar embryology. Therefore “evolution” is true. This fails because embryology is expected to match genetics and morphology, hence the previous counterargument applies.
    • If “evolution” is true, one might expect vestigial organs. What looks like vestigial organs can be observed. Therefore “evolution” is true. This fails because what if those organs are useful rather that “vestigial”? And why would “evolution” not do away with “vestigial” organs as soon as they become useless? In sum, why can’t these organs have another reason or origin than “evolution”?
    • If “evolution” is true, one expects adaptability such as antibiotic resistance. Antibiotic resistance is observed. Therefore “evolution” is true. This fails because adaptabilities such as antibiotic resistance are compatible with other hypotheses, not just “evolution”. In addition, antibiotic resistance is ubiquitous, limited, reversible, and never observed to result in organism transmutation aka “evolution”.
  4. How can “proofs of evolution” avoid the ‘Affirming the Consequent’ logical fallacy? Direct confirmation of “evolution” is unlikely as shown by the LTEE study. Alternatively, an observation that is true for “evolution” and only for “evolution” might also work. In other words, what’s missing from all the examples above is a true statement of the kind: “only if evolution is true, then XYZ”. Of course, excluding all alternatives to “evolution” is an impossible task therefore, given that Intelligent Design is the main rival, proponents of “evolution” need only add a true statement of the kind: “if Intelligent Design is true, then XYZ is not true” to turn their invalid arguments into valid ones. But even this lower bar cannot be met by “evolution” proponents, thus making all “proofs of evolution” invalid.
  5. Isn’t then all science ‘Affirming the Consequent’? For example, “if Newtonian physics is true, a ball thrown at angle Theta and speed V will land D meters away. The experiment is carried out, and we find that the ball landed distance D away. Therefor physics is true.” No! This is not a fallacy because it meets the “if and only if” requirement and is limited to “everything else equal” cases. Rockets do not disprove this claim because everything else is not equal between them and thrown inactive projectiles. In addition, no one claims a single experiment confirms all Newtonian Mechanics the way “proofs of evolution” are presented. In this case, multiple combinations of Angles and Speed result in the same Distance without violating Newtonian Mechanics because this experiment proves only portions of the theory.

Links:

https://en.wikipedia.org/wiki/Affirming_the_consequent

https://www.amazon.com/Biblical-Wisdom-Literature-Joseph-Koterski/dp/1598035258

http://myxo.css.msu.edu/ecoli/

ID journal silently revises article

The online intelligent-design journal, BIO-Complexity (Robert J. Marks II, editor-in-chief; Douglas Axe, managing editor), has revised at least one of its published articles without giving any indication of change. “A Unified Model of Complex Specified Information,” by George D. Montañez, states that it was published on December 14, 2018, and makes no note of having been revised since. However, the article presently has two more entries in the reference list than it did on December 17, 2018, when I downloaded it. The announcments page of the journal says nothing about the change.

BIO-Complexity claims to be an archival publication. Thus the content should not change at all once it is released. The editors have given us reason to wonder how much of journal has silently morphed over the years. They should have required the author to submit an erratum or an addendum, no matter how benign the changes he wanted to make to the article.

I suspect, but cannot be sure, that Montañez changed the article merely to give credit to A. Milosavljević for a theorem, after learning of it from my post “Evo-Info 4: Non-Conservation of Algorithmic Specified Complexity.” If that is the case, then Montañez should have submitted an addendum explaining that he had learned of the theorem from me after his article was published. Changes to supposedly archival material are wrong even when announced, and are doubly wrong when unannounced.

It now behooves the editors of BIO-Complexity to make an announcement detailing the changes to Montañez’s article, and indicating whether any other articles have been modified since publication. If they have any sense at all, then they will announce also that they will never again change material that they represent as archival.